The paper can be logically divided into two parts. In the first part I distinguish two kinds of metaphysics: basic metaphysics, which affects scientific theories, and a second kind, which is an effect of interpretations of these theories. I try to show the strong mutual relations between metaphysics and science and to point out that the basic metaphysics of science is based on realistic assumptions. In the second part of my paper I suggest that we should consider the basic metaphysics of science and its realistic foundations in order to better understand scientific realism and to properly resolve the debate around it. The methodology of Imre Lakatos is applied in the paper.